From f1cd3af86dc38a3ce4eadaf4a52d441c7bd7feaf Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Thu, 30 Nov 2023 12:51:21 +0100
Subject: [PATCH] comet tsv file parsing not implemented yet

---
 .../parser/InputFileParserFactory.java        | 34 +------------------
 1 file changed, 1 insertion(+), 33 deletions(-)

diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/parser/InputFileParserFactory.java b/src/main/java/de/mpc/pia/intermediate/compiler/parser/InputFileParserFactory.java
index 2162415..cbdd9b9 100755
--- a/src/main/java/de/mpc/pia/intermediate/compiler/parser/InputFileParserFactory.java
+++ b/src/main/java/de/mpc/pia/intermediate/compiler/parser/InputFileParserFactory.java
@@ -9,7 +9,7 @@
 import org.apache.logging.log4j.Logger;
 
 import de.mpc.pia.intermediate.compiler.PIACompiler;
-import de.mpc.pia.intermediate.compiler.parser.searchengines.CometCSVFileParser;
+import de.mpc.pia.intermediate.compiler.parser.searchengines.CometTSVFileParser;
 import de.mpc.pia.intermediate.compiler.parser.searchengines.MascotDatFileParser;
 import de.mpc.pia.intermediate.compiler.parser.searchengines.TandemFileParser;
 import de.mpc.pia.intermediate.compiler.parser.searchengines.ThermoMSFFileParser;
@@ -21,38 +21,6 @@ public class InputFileParserFactory {
 	private static final Logger LOGGER = LogManager.getLogger();
 
     public enum InputFileTypes {
-
-        /**
-         * the input file is a Tide TXT file
-         */
-        COMET_CSV_INPUT {
-            @Override
-            public String getFileSuffix() {
-                return "csv";
-            }
-
-            @Override
-            public String getFileTypeName() {
-                return "Comet CSV";
-            }
-
-            @Override
-            public String getFileTypeShort() {
-                return "comet";
-            }
-
-            @Override
-            public boolean checkFileType(String fileName) {
-                return CometCSVFileParser.checkFileType(fileName);
-            }
-
-            @Override
-            public boolean parseFile(String name, String fileName,
-                    PIACompiler compiler, String additionalInfoFileName) {
-                return CometCSVFileParser.getDataFromCometCSVFile(name, fileName, compiler);
-            }
-        },
-
         /**
          * the input file is a FASTA database file
          */